In simecek/HPQTL2: HPQTL2

library(HPQTL2)
library(microbenchmark)

cross <- sim.geno.f2(250)
G <- gensim(cross$X, cross$markers)
Glist <- gensim(cross$X, cross$markers, "LOCO")
Glist2 <- gensim(cross$X, cross$markers, "POMOLOCO")

set.seed(123)
pheno <- sim.pheno(cross$X, G, 0.5)

microbenchmark(
  fit.lm = scan.lm(pheno, cross$X, cross$markers),
  fit.lmm = scan.lmm(pheno, cross$X, cross$markers, G=G),
  fit.loco = scan.loco(pheno, cross$X, cross$markers, Glist=Glist),
  fit.pomo = scan.pomo(pheno, cross$X, cross$markers, G=G),
#  fit.pomoloco = scan.pomoloco(pheno, cross$X, cross$markers, Glist=Glist2),
#  fit.pomoloco2 = scan.pomoloco(pheno, cross$X, cross$markers, Glist=Glist2, faster = FALSE),
  times = 5
)

simecek/HPQTL2 documentation built on May 29, 2019, 10:01 p.m.